On Sat, May 7, 2011 at 6:01 AM, souvik sur <souviksur.hotmail.com> wrote:
>
> Dear sir,
> Thank you for your kind concern,I was trying with the following commands
> for running antechamber in my system,after
> downloading AmberTools-1.5:
>
Ah, I didn't see that this was actually AmberTools 1.5. The error that you
got was for antechamber from amber9 (the new one will never call divcon).
Make sure you're using the correct antechamber (this is a general UNIX
issue).
>
> $ tar jxvf ~/Download/AmberTools-1.5.tar.bz2 -C /opt$ ./configure
> -macAccelerate gn
> $ make
> $ cd ../test
> $ cd ../src
>
> $ make clean
>
> after the command "clean" there showed no error and also it was passed the
> "test" command showing no error.After doing all the things, then I tried to
> run "sustiva" for antechamber but then it showed:
>
> [root.localhost ~/souvik]# $AMBERHOME/exe/antechamber -i sustiva.pdb -fi
> pdb -o sustiva.prepin -fo prepi -c bcc -s 2
> Running: /usr/local/amber9/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o
> ANTECHAMBER_BOND_TYPE.AC -f ac -j full
>
>
> Running: /usr/local/amber9/exe/atomtype -i ANTECHAMBER_AC.AC0 -o
> ANTECHAMBER_AC.AC -p gaff
>
> Total number of electrons: 160; net charge: 0
>
> Running: $AMBERHOME/exe/divcon
> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> Image PC Routine Line Source
> divcon 08336186 Unknown Unknown Unknown
> divcon 081F4BE0 Unknown Unknown Unknown
> divcon 081BE548 Unknown Unknown Unknown
> Error: cannot run "$AMBERHOME/exe/divcon" of bcc() in charge.c properly,
> exit
>
> Can I able to understand my problem now?
>
>
> regards,
> Souvik Sur
> Ph. D. Student
> Department Of Chemistry
> University Of Delhi
> India
>
>
>
>
> > Date: Fri, 6 May 2011 10:02:01 -0400
> > From: case.biomaps.rutgers.edu
> > To: amber.ambermd.org
> > Subject: Re: [AMBER] Antechamber loading Problem
> >
> > On Fri, May 06, 2011, souvik sur wrote:
> > >
> > > Unknown UnknownError: cannot run "$AMBERHOME/exe/divcon"
> >
> > As you already know, you need to upgrade.
> >
> > > already untarred the AmberTools 1.5 tar file and also compiled
> > > openmpi-1.4 tar file which is
> > > needed for installation.
> >
> > First, openmpi (or any MPI) has nothing to do with antechamber. Second,
> > you don't tell us what you did after untarring the AmberTools 1.5 file,
> how
> > you configured and compiled it, or what the problem is with the new code.
> > You also don't say (in any of these messages) anything about the results
> of
> > running the test suite. I can guess(!?!) that you came across sustiva in
> the
> > test suite, but this is only a guess, and there is no information given
> about
> > the results of any other tests.
> >
> > So, please put just one question in each email, and *carefully* describe
> > exactly what you did, and exactly what the result was. Don't do anything
> with
> > parallel options until you understand how the serial codes work.
> >
> > ....dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sat May 07 2011 - 04:00:03 PDT
